VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Thu Jan 17 2008 - 00:49:37 CST

I am carrying out MD of a protein-ligand (the latter non polymeric, large) in a
POPC membrane. Things run satisfactorily, though I was unable to gather all
information that should be possible.

The ligand has O-hetero-rings, so that in visualizing rmsd with the RMDS traj
Tool I would like to have the oxygen atom included. What I did in the window
was to replace on top left box "protein" with "resname XYZ", where XYZ is the
name of the ligand. I got the plot with the top indication (in red) "RMSD vs
Frame "(resname XYZ) and name C CA N". This ligand has no aromatic carbons, nor
nitrogen atoms. It has sp3 and sp2 carbons and ethereal oxygen. Where should I
set these indications?

I know I should educate myself throughly on VMD. Time is short.

Thanks
francesco pietra

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